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UC Davis Genome Center
University of California
One Shields Avenue
Davis, CA 95616
(530) 754-9647 (Office)
(530) 754-9658 (FAX)
cjbenham@ucdavis.edu
Education
Swarthmore College 1964-1968 A.B. Mathematics
Princeton University 1968-1971 M.A. Mathematics
Princeton University 1971-1972 Ph.D. Mathematics
My thesis was in Complex Manifold Theory; my doctoral advisor was Dr. Robert Gunning.
Postdoctoral Training
Research Fellow with Dr. Max Delbrück, Biology Division, Caltech, 7/76 - 8/77
Academic Appointments
Professor of Biomedical Engineering University of California at Davis 7/01 - present
Professor of Mathematics University of California at Davis 7/01 - present
Professor of Biomathematical Sciences Mount Sinai School of Medicine 7/88 - 6/01
Associate Professor of Mathematics University of Kentucky 7/81 - 6/88
Assistant Professor of Mathematics University of Kentucky 9/78 - 6/81
Assistant Professor of Mathematics Lawrence University 9/77 - 6/78
Assistant Professor of Mathematics University of Notre Dame 9/72 - 6/76
Administrative Appointments
Associate Director for Bioinformatics UC Davis Genome Center 7/01 - present
Interim Director UC Davis Genome Center 7/01 - present
Acting Chair of Biomathematical Sciences Mount Sinai School of Medicine 1/90 - 6/01
Academic Honors
AB degree awarded with High Honors Swarthmore College June 1968
National Defense Education Act Fellowship Princeton University 1969 - 1972
Alfred P. Sloan Foundation Research Fellowship 1982 - 1985
Teaching Experience
Courses taught in the undergraduate mathematics curriculum include:
Algebra
Real Analysis
Complex Analysis
Topics in Applied Mathematics
Calculus, semesters I-IV
Differential Equations
Differential Geometry
Discrete Mathematics
Geometry
Linear Algebra
Logic
Mathematical Biology
Numerical Analysis
Numerical Linear Algebra
Statistics
Topology.
Mathematics courses taught at the graduate level include:
Mathematical Biology
Mathematical Modeling
Topology.
I developed the original curriculum for students in the graduate program of the Department of Biomathematical Sciences at Mount Sinai. I created and developed the syllabi for our courses in Mathematical Methods and in Computational Structural Biology. I have supervised the departmental Journal Club and Seminar Series, and have taught in the following courses at Mount Sinai, all of which are at the graduate level:
Advanced Topics in Biomathematical Sciences
Biophysics of Nucleic Acids and Proteins
Computational Structural Biology
Computers in Medicine (joint course with the CUNY CS Department)
Mathematical Methods
Mathematical Modeling.
Training of Doctoral Students and Postdocs
M. Saleet Jafri, Ph.D. received in 1993. Current position: Postdoctoral Associate, Johns
Hopkins University.
Hong-Zhi Sun, Ph.D. received in 1995. Current position: Postdoctoral Associate, Cornell
University.
Andrew Einstein, Ph.D. and M.D. both received in 1999. Current position: Resident, Robert
Wood Johnson Medical School.
Armando Solis, current student.
Yuguang Xiong, current student.
Peter Morrison, current postdoc.
Prashanth Ak, current postdoc.
Other Professional Activities
Member, Editorial Board, Journal of Computational Biology.
Member, Advisory Board, Nucleic Acid Database Project.
Peer Reviewer for the following journals:
Biochemistry
Biophysical Chemistry
Biophysical Journal
Biopolymers
Europhysics Letters
Journal of Biomolecular Structure and Dynamics
Journal of Molecular Biology
Journal of Theoretical Biology
Macromolecules
Mathematical Reviews
Molecular Microbiology
Physical Reviews
Proceedings of the National Academy of Sciences
Protein Science
Science.
Member, Program Committee, RECOMB98 - Second International Conference on
Computational Molecular Biology, New York
Member, Program Committee, SODA99 - Tenth Annual ACM-SIAM Symposium on
Discrete Algorithms.
Grant Reviewer for:
NIH - National Center for Human Genome Research. Member, Special Review Committee.
NIH - National Institute for General Medical Sciences. Ad hoc member, BBCA Study Section
NIH - Member, Special Study Section to evaluate Small Business Innovation Research Grants.
NSF - Member, Panel on the Theory of Computing
NSF - Member, Proposal Advisory Panel on Bio Research Training Groups
DOE - Member, both the Laboratory and the Extramural Review Panels on the Use of Model Organisms to Understand the Human Genome.
Member, National Research Council Panel on Mathematical Problems in Molecular
Modeling.
Member, National Research Council Panel on Epidemiology and Biostatistics.
External Reviewer, Program in Bioinformatics, German Cancer Research Center,
Heidelberg, Germany.
Member, Predoctoral Fellowships in Biological Sciences 1998 Evaluation Panel in
Biostatistics and Epidemiology, Howard Hughes Medical Institute.
Member, Predoctoral Fellowships in Biological Sciences Evaluation Panel in
Biochemistry and Structural Biology, Howard Hughes Medical Institute, 1999-2002
Member, Advisory Committee on Bioinformatics and Computational Molecular Biology,
Alfred P. Sloan Foundation.
Active Research Grants
NIH Research Grant RO1 GM47012, Theoretical Analysis of DNA Superhelical Equilibria, C. Benham, PI, 8/1/93 - 7/31/01, $1,056,271.
NSF Research Grant DBI-9904549, Stress-Induced DNA Denaturation in Regulation, C. Benham, PI, 9/1/99 - 8/31/02, $461,543.
NIH Research Grant RO1 HG01973, Inferring Chromosome Architecture from Genomic Sequence, C. Benham, PI, 4/1/00 - 3/31/03, $812,750.
Invited Talks, 1995 - 2001
Conferences
Topologically Driven Transit6ions in DNA Structure: Their Mathematical Analysis and Role in Biology, DIMACS Workshop on DNA Sequence and Topology, Rutgers University, Piscataway NJ, April 19-20, 2001.
The Central Role of DNA Structural Properties in Genomic Regulation, DIMACS Workshop on Whole Genome Comparisons, Rutgers University, Piscataway NJ, February 28 - March 2, 2001.
Analysis of the Global Role of IHF in Transcriptional Regulation, DIMACS Workshop on System Based Modelling in Bioinformatics, Rutgers University, Piscataway NJ, February 19-20, 2001.
Stress-Induced DNA Duplex Destabilization in Transcriptional Initiation, 2001 Pacific Symposium on Biocomputing, Hawaii, January 3-7, 2001.
Mathematical Aspects of DNA Structure, plenary keynote address, 16th IMACS World Congress, Lausanne, Switzerland, August 21-25, 2000.
Global Control of Gene Expression through Superhelical DNA Destabilization, Asilomar 2000 Tryptophan Plus Conference, Asilomar CA, January 7-9, 2000.
Computational Analysis of Structural Transitions in Topologically Stressed DNA, Computational Biology Minisymposium, University of Texas at Dallas, October 11, 1999.
Superhelical Duplex Destabilization and DNA Regulation, First Cold Spring Harbor Annual Meeting on Computational Biology, Cold Spring Harbor Labs, NY, September 7-9, 1999.
A New Computational Strategy for Searching Genomic DNA Sequences for Regulatory Regions, Invited Lecture, SIAM Annual Meeting, Atlanta, GA, May 14, 1999.
Structural Transitions in Superhelical DNA, Invited Talk, Meeting on The Role of DNA Topology, Conformation and Associated Factors in Gene Expression, Banbury Center, Cold Spring Harbor Labs, March 16, 1999.
Macromolecular Properties of DNA, Invited Address, 1998 Princeton Lectures on Biophysics, NEC Research Institute, Princeton, NJ, June 21-25, 1998.
The Future of Computational Biology - Perils and Promise, 1997 Inaugural Lecture, DIMACS Computational Biology Seminar Series, Rutgers University, October 15, 1997.
Superhelical Transitions and DNA Regulation, Invited address, Second DIMACS Workshop on DNA Topology, Rutgers University, April 3-4, 1997
Sites of Superhelical DNA Destabilization Occur at Specific Regulatory Regions, Invited Plenary Lecture, workshop on Molecular Structure: Dynamics, Geometry and Topology, Institute for Mathematics and its Applications, Minneapolis MN, January 20-23, 1997.
Sites of Superhelical Duplex DNA Destabilization Occur at Specific Regulatory Regions, 1996 German Conference on Bioinformatics, Leipzig, Germany, September, 1996.
The Past and Future of Computational Biology, keynote address, Conference on Computational Biology in Commemoration of the 50th Anniversary of the ENIAC Computer, Princeton University, May, 1996.
Sites of Superhelical DNA Duplex Destabilization Occur at Specific Transcriptional Regulatory Regions, Invited Lecture, International Workshop on the Computational Analysis of Eukaryotic Transcriptional Regulatory Elements, Heidelberg, Germany, January, 1996.
Computation of DNA Structural Variability - New Tools for Predicting DNA Regulatory Regions, Invited Address, Discussion Meeting on Computational Biology, sponsored by the Jawaharlal Nehru Center for Advanced Scientific Research, Bangalore India, December, 1995.
Sites of Superhelical DNA Duplex Destabilization Occur at Transcriptional Regulatory Regions, Invited Lecture, 4th Symposium on Mathematics and Molecular Biology, Santa Fe, NM, November, 1995.
Sites of Superhelical DNA Duplex Destabilization Occur at Transcriptional Regulatory Regions, DIMACS Workshop on Gene Finding and Gene Structure Prediction, Philadelphia, PA, October, 1995.
Of Chicken Teeth in Mouse Eyes, or Generalized Character Compatibility, 6th International Symposium on Combinatorial Pattern Matching, Helsinki, Finland, July, 1995.
Session Chair, IEEE International Symposium on Intelligence in Neural and Biological Systems, Herndon VA, May, 1995.
Invited Participant, round table discussion on Physical and Computational Problems of DNA Sequencing, 73rd Statistical Mechanics Meeting, Rutgers University, Piscataway, NJ, May, 1995.
The Analysis of Topologically Stressed DNA Structures and their Energetics, Invited Address, Special Session on Scientific Applications of Geometry and Topology, American Mathematical Society Meeting, Orlando, FL, March 1995.
Seminars and Colloquia
Roles of DNA Duplex Destabilization in Gene Regulation, Research Seminar, Environmental and Occupational Health Sciences Institute, Rutgers University, April 18, 2001.
Stress-Induced Duplex Destabilization in DNA Regulation, Research Seminar, Merck and Co., Rahway, NJ, March 20, 2001.
Mechanisms of DNA Regulation Involving Stress-Induced Duplex Destabilization, Molecular Genetics and Microbiology Seminar, University of Texas, Austin TX, January 29, 2001.
Mechanisms of DNA Regulation Involving Stress-Induced Duplex Destabilization, Molecular Genetics and Microbiology Seminar, University of Texas, Austin TX, January 29, 2001.
Topologically Driven Structural Transitions in DNA - Their Mathematical Analysis and Roles in Biology, Distinguished Seminar Series on Bioinformatics and Computational Biology, University of Maryland, College Park MD, October 27, 2000.
The Central Role of DNA Structural Properties in Genomic Regulation, Research Seminar, Texas Institute for Computational Applied Mathematics, University of Texas, Austin, TX, October 10, 2000.
Topologically Driven Structural Transitions in DNA - Their Mathematical Analysis and Roles in Biology, Mathematics Colloquium, University of Texas, Austin, TX, October 9, 2000.
Topologically Driven Structural Transitions in DNA - Their Mathematical Analysis and Roles in Regulation, Mathematics Colloquium, University of Michigan, Ann Arbor, MI, September 19, 2000.
Topologically Driven Structural Transitions in DNA: Their Analysis and Biological Functions, invited colloquium talk, session on Continuum Mechanics of DNA, 16th IMACS World Congress, Lausanne, Switzerland, August 21, 2000.
Future Opportunities in Computational Biology and Genomics, invited seminar, DARPA, Arlington, VA. August 8, 2000
Stress-Induced DNA Duplex Destabilization and its Roles in Various Regulatory Mechanisms, Biomedical Engineering Department Seminar, University of California at Davis, Davis, CA, May 25, 2000.
Topologically Driven Structural Transitions in DNA - Their Analysis and Roles in Gene Regulation, Mathematics Department Seminar, University of California at Davis, Davis, CA, May 24, 2000.
Superhelical DNA Duplex Destabilization - its Analysis and its Roles in Regulation, Bioinformatics Program Seminar, University of Michigan, Ann Arbor, MI, March 30, 2000.
Mathematical Aspects of DNA Structure, Mathematics Department Seminar, University of Michigan, Ann Arbor, MI, March 29, 2000.
Stress-Induced DNA Duplex Destabilization and its Roles in Regulation, Research Seminar, Cereon Genomics, Cambridge, MA, March 9, 2000.
Superhelically Induced DNA Duplex Destabilization and Regulation, Research Seminar, National Institutes of Health, Bethesda, MD, February 17, 2000.
Structural Transitions in DNA Regulation, Computer Sciences Department Seminar, Virginia Polytechnical Institute and State University, Blacksburg, VA, January 18, 2000.
The Promise and Perils of Computational Biology, Mathematics Department Seminar, Salve Regina College, Newport, RI, December 2, 1999.
Roles of Structural Transitions in DNA Regulation, Mathematics Department Seminar, University of Southern California, November 18, 1999.
Superhelical DNA Duplex Destabilization in Transcription, Replication and Chromosome Organization, Seminar on Computational Biology, Institute for Cellular and Molecular Biology, University of Texas, October 14, 1999.
DNA Topology and Mechanics, Research Seminar, Department of Mathematics, University of Texas, October 13, 1999.
Structural Transitions in Topologically Constrained DNA: Their Mathematical Analysis and Roles in Regulation, Texas Institute for Computational Applied Mathematics, University of Texas, October 12, 1999.
The Emergence of Mathematical Biology - New Opportunities and Old Pitfalls, Colloquium, Mathematics Department, Rutgers University, September 24, 1999.
DNA Structure and Flexibility - Inferences from the Crystal Structure Database, Research Seminar, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland, July 1, 1999.
Structural Transitions in Topologically Constrained DNA: Their Mathematical Analysis and Roles in Regulation, Research Seminar, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland, June 30, 1999.
Structural Transitions in Topologically Constrained DNA: Their Mathematical Analysis and Roles in Regulation, Research Seminar, UC Santa Cruz, May 7, 1999.
A New Computational Method to Find Structural Correlates of DNA Regulatory Regions, Research Seminar, Computer Science Department, University of Arizona, Tucson, AZ, November 17, 1998.
Structural Aspects of DNA Regulation, Research Colloquium, Department of Physics, City College, NYC, September 9, 1998.
Macromolecular Properties of DNA, Invited Address, 1998 Princeton Lectures on Biophysics, NEC Research Institute, Princeton, NJ, June 21-25, 1998.
Stress-Induced DNA Duplex Destabilization as a Predictor of Regulatory Activity, Research Seminar, SmithKline Beecham Pharmaceutical Corp., Upper Merion, PA, April 10, 1998.
Structural Transitions in Topologically Constrained DNA, Applied Mathematics Research Seminar, Princeton University, March 30, 1998.
Stress-Induced Destabilization of the DNA Double Helix, Biomedical Engineering Research Seminar, University of California, Davis, March 13, 1998.
Sites of Superhelical DNA Duplex Destabilization Occur at Specific Regulatory Regions, Seminar, Computer Science Department, University of California, Irvine, January 30, 1998.
Strand Separation in Topologically Constrained DNA: Methods of Analysis and Roles in Regulation, Seminar, Applied Mathematics Department, Caltech, January 28, 1998.
DNA Duplex Destabilization and Regulation, Seminar, Lawrence Berkeley Labs, January 26, 1998.
Computational Analysis of Structural Transitions in Stressed DNA - A New Predictor of Regulatory Regions, GBF Colloquium, Gesellschaft für Biotechnologische Forschung, Braunschweig, Germany, November 6, 1997.
The Future of Computational Biology - Perils and Promise, 1997 Inaugural Lecture, DIMACS Computational Biology Seminar Series, Rutgers University, October 15, 1997. Participant and Speaker, Workshop on Identifying Features in Biological Sequences, Aspen Center for Physics, June 9-21, 1997.
Superhelicity and DNA Tertiary Structure, invited presentation to the scientist in Dr. John Maddocks' research group, University of Maryland, May 26, 1997.
Superhelical Transitions and DNA Regulation, Invited address, Second DIMACS Workshop on DNA Topology, Rutgers University, April 3-4 1997
Structural Transitions in Supercoiled DNA, Seminar, Center for Studies in Physics and Biology, Rockefeller University, February 25, 1997
Sites of Superhelical DNA Destabilization Occur at Specific Regulatory Regions, Invited Plenary Lecture, workshop on Molecular Structure: Dynamics, Geometry and Topology, Institute for Mathematics and its Applications, Minneapolis, MN, January 20-23, 1997.
DNA Duplex Destabilization and Regulation, Research Seminar, Scripps Institute, La Jolla, CA, December, 1996
Superhelical DNA Duplex Destabilization as a Predictor of Regulation, Research Seminar, Department of Microbiology and Molecular Genetics, UC Irvine, Irvine, CA, December, 1996.
New Strategies to Search Genomic DNA Sequences for Regulatory Regions, Research Seminar, Computational Biology Program, Department of Mathematics, University of Southern California, Los Angeles, CA, December, 1996.
Sites of Predicted Duplex DNA Destabilization Occur at Specific Regulatory Regions, Research Seminar, National Institutes of Health, Bethesda, MD, October, 1996.
DNA Strand Separation and Regulation, Research Seminar, GBF - Braunschweig, Germany, October, 1996.
Stress-Induced Transitions and DNA Regulation, Research Seminar, Department of Chemistry, Cornell University, Ithaca NY, Septembe, 1996.
Stress-Induced Strand Separation and the Regulation of DNA, Research Seminar, Department of Molecular Biology, University of Valencia, Valencia, Spain, July, 1996.
Beyond Sequence - Physical-Chemical Correlates of DNA Regulatory Activity, Conference on Computational Biology in Commemoration of the 50th Anniversary of the ENIAC Computer, Princeton University, May, 1996.
Physical Correlates of DNA Regulatory Regions, Department of Genetics Seminar, Mount Sinai School of Medicine, New York, April, 1996.
Mathematical Aspects of DNA Structure and Function, Mathematics Department Colloquium, University of Pennsylvania, Philadelphia, PA, February, 1996.
Stress-Induced Structural Transitions in DNA, Research Seminar, IBM T.J.Watson Research Labs, Yorktown Heights, NY, January, 1996.
Computational Analysis of Structural Transitions in Stressed DNA, Computer Science Department Research Colloquium, Princeton University, Princeton, NJ, November, 1995.
Computation in Biology - New Opportunities and Old Pitfalls, Computer Science Department Seminar, Princeton University, Princeton, NJ, November, 1995.
Computational Methods to Analyze Supercoiled DNA, Research Colloquium, Sandia National Labs, Albuquerque, NM, January, 1995.
Research Publications
1. Kozak, J. and Benham, C. (1974) Denaturation: An Example of a Catastrophe, Proc. Nat'l. Acad. Sci. USA 71: 1977-1981.
2. Benham, C. and Kozak, J. (1976) Denaturation: An Example of a Catastrophe II - Two-State Transitions, J. Theor. Biol. 83: 125-149.
3. Benham, C. and Kozak, J. (1977) Denaturation: An Example of a Catastrophe III - Phase Diagrams for Multistate Transitions, J. Theor. Biol. 88: 679-693.
4. Benham, C. (1977) Elastic Model of Supercoiling, Proc. Nat'l. Acad. Sci. USA 74: 2397-2401.
5. Benham, C. (1978) The Statistics of Superhelicity, J. Mol. Biol. 123: 361-370.
6. Benham, C. and Kozak, J. (1978) Catastrophes in Statistical Biophysics, Behavioral Science 23: 355-359.
7. Benham, C. (1979) An Elastic Model of the Large-Scale Structure of Duplex DNA, Biopolymers 18: 609-623.
8. Benham, C. (1979) Torsional Stress and Local Denaturation in Supercoiled DNA, Proc. Nat'l. Acad. Sci. USA 76: 3870-3874.
9. Benham, C., Brady, G. and Fein, D. (1979) X-ray Scattering from Randomly Oriented Superhelices, Biophysical J. 29: 351-366.
10. Benham, C. (1980) The Equilibrium Statistical Mechanics of the Helix-Coil Transition in Torsionally Stressed DNA, J. Chem. Phys. 72: 3633-3639.
11. Benham, C. (1980) Theoretical Analysis of Transitions between B- and Z Conformations in Torsionally Stressed DNA, Nature 288: 637-638.
12. Benham, C. (1980) The Kinetics of Reactions Involving DNA Containing Stress induced Single Stranded Regions, Biopolymers 10: 2143-2164.
13. Benham, C. (1981) The Fourier Transforms of a Coiled Coil and a Toroidal Helix, Acta Cryst. A 37: 309-314.
14. Benham, C. (1981) A Theoretical Analysis of Competing Conformational Transitions in Torsionally Stressed DNA, J. Mol. Biol. 150: 43-68.
15. Crowley, P., Benham, C., Lenhart, S. and Morgan, J. (1981) Peripheral Doublet Microtubules and Wave Generation in Eucaryotic Flagella, J. Theor. Biol. 93: 769-784.
16. Benham, C. (1982) Stable Cruciform Formation at Inverted Repeat Sequences in Supercoiled DNA, Biopolymers 21: 679-693.
17. Benham, C. (1982) Statistical Mechanical Analysis of Competing Conformational Transitions in Superhelical DNA, Cold Spring Harbor Symposium on Quantitative Biology 47: 219-227.
18. Grassian, V. Brady, G. and Benham, C. (1983) X-ray Conformational Study of the DNA Duplex in Solution, Biopolymers 22: 1523-1543.
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19. Brady, G., Fein, D., Lambertson, H., Grassian, V., Foos, D., and Benham, C. (1983) X-ray Scattering from the Superhelix in Circular DNA, Proc. Nat'l. Acad. Sci. USA 80: 741-744.
20. Benham, C. (1983) The Cylindrical Poisson-Boltzmann Equation I: Transformations and General Solutions, J. Chem. Phys. 79: 1969-1973.
21. Benham, C. (1983) Geometry and Mechanics of DNA Superhelicity, Biopolymers 22: 2477-2495.
22. Brady, G., Foos, D. and Benham, C. (1984) Evidence for an Interwound Form for the Superhelix in Circular DNA, Biopolymers 23: 2963-2966.
23. Benham, C. (1985) The Theoretical Analysis of Conformational Equilibria in Superhelical DNA, Ann. Rev. Biophys. Biophys. Chem. 14: 23-45.
24. Brady, G., Satkowski, M., Foos, D., and Benham, C.J. (1986) Ionic Strength and Temperature Effects on the Superhelix Conformation in Solution, Biomolecular Stereodynamics IV, Adenine Press, 63-74.
25. Benham, C.J. (1987) The Role of the Stress Resultant in Determining Mechanical Equilibria of Superhelical DNA, Biopolymers 28: 9-15.
26. Benham, C.J., (1987) The Energetics of Superhelicity and of B-Z Transitions in Superhelical DNA, Cell Biophys. 10: 193-204.
27. Brady, G., Foos, D., Satkowski, M., and Benham, C. (1987) Environmental Influences on DNA Superhelicity: The E_ect of Ionic Strength on Superhelix Conformation in Solution, J. Mol. Biol. 195: 185-191.
28. Benham, C.J. (1987) The Influence of Tertiary Structural Restraints on Conformational Transitions in Superhelical DNA, Nuc. Acids Res. 15: 9985-9995.
29. Benham, C.J., (1989) Onset of Writhing in Circular Elastic Polymers, Phys. Rev. A 39: 2582-2586.
30. Benham, C.J., (1990) Free Energies Associated with Superhelical Deformations of DNA, in Proceedings of the 6th Conversation on Biomolecular Stereodynamics, edited by R. Sarma and M. Sarma, Adenine Press, 3: 255-266.
31. Benham, C.J., (1990) Theoretical Analysis of Heteropolymeric Transitions in Superhelical DNA Molecules of Specified Sequence, Journal of Chemical Physics 92: 6294-6305.
32. Miller, J., Nelson, J., Ye, M., Swenberg, C., Speicher, J. and Benham, C.J. (1991) Negative Supercoiling Increases the Sensitivity of Plasmid DNA to Single-Strand-Break Induction by X-Rays, Int'l. J. Rad. Biol. 59: 941-949.
33. Enami, M., Sharma, G., Benham, C. and Palese, P. (1991) An Influenza Virus Containing Nine Different RNA Segments, J. Virology. 185: 291-298.
34. Benham, C.J. (1992) The Energetics of the Strand Separation Transition in Superhelical DNA, J. Mol. Biol. 225: 835-847.
35. Magarshak, Y. and Benham, C.J. (1992) An Algebraic Representation of RNA Secondary Structures, J. Biomolec. Struct. Dyn. 10: 465-488.
36. Magarshak, Y., Benham, C., Malinsky, J. and Blumenfeld, L. (1993) Dynamics of Secondary Structure of RNA and Symmetry of Genetic Vectors, Biophysics (Russia) 38:98-107.
37. Benham, C. J. and Jafri, M. S. (1993) Disulphide Bonding Patterns and Protein Topologies, Protein Science. 2: 41-54.
38. Benham, C.J. (1993) Sites of Predicted Stress-Induced DNA Duplex Destabilization Occur Preferentially at Regulatory Loci, Proc. Nat'l. Acad. Sci. USA. 90: 2999-3003.
39. Bauer, W.R. and Benham, C.J. (1993) The Free Energy, Enthalpy and Entropy of Native and of Partially Denatured Closed Circular DNA, J. Mol. Biol. 234: 1184-1196.
40. Sioud, M., Opstad, A., Zhao, J.-Q., Levitz, R., Benham, C.J. and Drlica, K. (1994) In vivo Decay Kinetic Parameters of Hammerhead Ribozymes, Nuc. Acids Res. 22:5571-5575.
41. Benham, C.J., Kannan, S. and Warnow, T. (1995) Of Chicken Teeth and Mouse Eyes, or Generalized Character Compatibility, Proceedings of the 6th Annual Symposium on Combinatorial Pattern Matching, CPM95, Z. Galil and E. Ukkonen, eds., Springer Verlag, Berlin, pp. 17-26 (refereed).
42. Bauer, W.R., Ohtsubo, H., Ohtsubo, E. and Benham, C.J. (1995) Energetics of Coupled Twist and Writhe Changes in Closed Circular pSM1 DNA, J. Mol. Biol. 253: 438-452.
43. Sun, H., Mezei, M., Fye, R. and Benham, C.J. (1995) Monte Carlo Analysis of Conformational Transitions in Superhelical DNA, J. Chem. Phys. 103: 8653-8665.
44. Benham, C.J., Kannan, S., Paterson, M. and Warnow, T. (1995) Hen's Teeth and Whale's Feet: Generalized Characters and their Compatibility, J. Comp. Biol. 2: 515-525.
45. Benham, C.J. (1996) Duplex Destabilization in Superhelical DNA is Predicted to Occur at Specific Transcriptional Regulatory Regions, J. Mol. Biol. 255: 425-434.
46. Benham, C.J. (1996) Theoretical Analysis of the Helix-Coil Transition in Positively Superhelical DNA at High Temperatures, Phys. Rev. E 53: 2984-2987.
47. Miller, D. and Benham, C.J. (1996) Fixed-Writhe Isotopies and the Topological Conservation Law for Closed Circular DNA, J. Knot Theory 5: 859-866.
48. Benham, C.J. (1996) Computation of DNA Structural Variability - A New Predictor of DNA Regulatory Regions, CABIOS - Comp. App. in Biol. Sci. 12: 375-381.
49. Miller, J.H., Nelson, J.M., Fleck, E. and Benham, C.J. (1996) Effects of Torsional Stress on the Interaction of DNA with Radiation and Chemicals, Appl. Occup. Environ. Hyg. 11, 417-420.
50. Aranda, A., Perez-Ortin, J., Benham, C.J. and del Olmo, M. (1997) Analysis of the in vivo Structure of a Natural Alternating d(TA)n Sequence in Yeast, Yeast 13, 313-326.
51. Hristescu, G., Benham, C.J., and Farach, M. (1997) DNA Strand Separation Prediction: A Parallel Implementation, Proceedings of the International Conference on Parallel and Distributed Processing Techniques and Applications, 2: 610-619 (refereed).
52. Benham, C.J., Kohwi-Shigematsu, T. and Bode, J. (1997) Stress-Induced Duplex Destabilization in Chromosomal Scaffold/Matrix Attachment Regions, J. Mol. Biol. 274: 181-196.
53. Bode, J., Bartsch, J., Boulikas, T., Iber, M., Mielke, C., Schübler, D., Seibler, J. and Benham, C.J. (1998) Transcription-Promoting Genomic Sites in Mammalia: Their Elucidation and Architectural Principles, Gene Ther. Mol. Biol. 1: 551-580.
54. Sheridan, S., Benham, C.J. and Hatfield, G.W. (1998) Activation of Gene Expression by a Novel DNA Structural Transmission Mechanism that Requires Supercoiling-Induced DNA Duplex Destabilization in an Upstream Activating Sequence, J. Biol. Chem. 273: 21298-21308.
55. Fye, R.M. and Benham, C.J. (1998) A Formally Exact Method to Numerically Analyze Local Denaturation in Superhelical DNA, Proceedings of the Second International Conference on Computational Molecular Biology, 79-84 (refereed).
56. Benham, C.J. (1999) The Topologically Driven Strand Separation Transition in DNA- Methods of Analysis and Biological Significance, DIMACS Series in Discrete Mathematics and Theoretical Computer Science 47: 173-198.
57. Fye, R.M. and Benham, C.J. (1999) Exact Method for Numerically Analyzing a Model of Local Denaturation in Superhelically Stressed DNA, Phys. Rev. E 59: 3408-3426.
58. Sheridan, S., Benham, C.J. and Hatfield, G.W. (1999) Inhibition of DNA Supercoiling-Dependent Transcriptional Activation by a Distant B-DNA to Z-DNA Transition, J. Biol. Chem. 274: 8169-8174.
59. Messmer, B., Benham, C.J. and Thaler, D. (2000) Sequential Determination of Ligands Binding to Discrete Components in Heterogeneous Mixtures by Iterative Panning and Blocking (IPAB), J. Mol. Biol. 296: 821-832.
60. He, L., Liu, J., Collins, I., Sanford, S., O'Connell, B., Benham, C.J., and Levens, D. (2000) Loss of FBP Function Arrests Cellular Proliferation and Extinguishes c-myc Expression, EMBO J. 19: 1034-1044.
61. Baiker, A., Maercker, C., Piechaczek, C., Schmidt, S., Bode, J., Benham, C.J. and Lipps, H.L. (2000) Mitotic Stability of an Episomal Vector Containing a Human Scaffold/Matrix-Attached Region is Provided by Nuclear Matrix Association, Nature - Cell Biol. 2:182-184.
62. Bode, J., Benham, C.J., Knopp, A. and Mielke, C. (2000) Transcriptional Augmentation: Modulation of Gene Expression by Scaffold/Matrix Attached Regions (S/MAR Elements), Crit. Rev. Euk. Gene Expr. 10: 73-90.
63. Benham, C.J. and Miller, D. (2000) Writhing and Linking Densities for Closed Circular DNA, J. Knot Theory 9: 577-585.
64. Leblanc, B., Benham, C.J., and Clark, D. (2000) An Initiation Element in the Yeast CUP1 Promoter is Recognized by RNA Polymerase II in the Absence of TATA boxbinding Protein if the DNA is Negatively Supercoiled, Proc. Nat'l. Acad. Sci. USA 97:10745-10750.
65. Bode, J., Benham, C.J., Ernst, E., Knopp, A., Marschalek, R., Strick, R. and Strissel, P. (2000) Fatal Connections: When DNA Ends Meet on the Nuclear Matrix, J. Cell. Biochem. 35: 3-22.
66. Benham, C.J. (2001) Stress-Induced DNA Duplex Destabilization in Transcriptional Regulation, Proceedings of the 2001 Pacific Symposium on Biocomputing (refereed), World Scientific, 103-114.
67. Benham, C.J., Lin, X.-S. and Miller, D. (2001) Subspaces of Knot Spaces, Proc. Amer. Math. Soc. 129: 3121-3127.
68. Engel, H., Ruehl, H., Benham, C.J., Bode, J., and Weiss, S. (2001) Germ-line Transcripts of the Immunoglobulin _ J-C Clusters in the Mouse: Characterization of the Initiation Sites and Regulatory Elements, Mol. Immunol. 38: 289-302.
69. Woynarowski, J.M., Trevino, A., Rodriguez, K., Hardies, S.C. and Benham, C.J. (2001) AT-rich Islands in Genomic DNA - A Novel Target for AT-specific DNA-reactive Antitumor Drugs, J. Biol. Chem. 276: 40555-40566.
70. Mielke, C., Christensen, M., Westergaard, O., Bode, J., Benham, C.J. and Breindl, M. (2002) Multiple Collagen I Gene Regulatory Elements Have Sites of Stress-Induced DNA Duplex Destabilization and Nuclear Scaffold/Matrix Association Potential, J. Cell. Biochem. 84: 484-496.
71. Benham, C.J., Savitt, A. and Bauer, W.R. (2002) Extrusion of an Imperfect Palindrome to a Cruciform in Superhelical DNA: Complete Determination of Energetics Based Upon a Statistical Mechanical Model, J. Mol. Biol. 316: 563-580.
72. Bode, J., Fetzer, C., Nehlsen, K., Scinteie, M., Hinrichs, B.-H., Baiker, A., Piechaczek, C., Benham, C.J. and Lipps, H.J. (2002) The Hitchhiking Principle: Optimizing Episomal Vectors for Use in Gene Therapy and Biotechnology, Gene Ther. Mol. Biol. To appear.
73. Mistry, S.J., Benham, C.J., and Atweh, G.F. (2002) Development of Novel Anti-Strathmin Ribozyme Based Strategies for the Gene Therapy of Cancer, submitted.
Unrefereed Publications
1. Benham, C. (1984) Theory of DNA Superhelicity, Springer-Verlag Lecture Notes in Biomathematics 47: 253-259.
2. Benham, C.J. (1986) Superhelical DNA, Comments Molec. Cell. Biophys. 4: 35-54.
3. Benham, C.J., (1988) Mechanics and Equilibria of Superhelical DNA, in Mathematical Methods for DNA Sequences, edited by M. Waterman, CRC Press, pp.255-277.
4. Benham, C.J., (1990) Superhelical Transitions and DNA Regulation, in Computers and DNA, edited by G. Bell and T. Marr, Addison-Wesley, Reading MA, pp. 139-146.
5. Benham, C.J. (1995) Unwinding the Double Helix: Using Statistical Mechanics to Probe Conformational Changes in DNA, Chapter 7 of Calculating the Secrets of Life: Applications of the Mathematical Sciences in Molecular Biology, E. Lander and M.S. Waterman, eds., National Academy Press, Washington, D.C., pp. 179-201.
6. Benham, C.J. (1997) Prediction of DNA Structural Variability - A New Computational Method for Finding DNA Regulatory Regions, in Some New Directions in Science on Computers, edited by Bhanot, Chen and Seiden, World Scientific, Singapore, pp.203-227.
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